Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sc8-pr-cvs5.sourceforge.net:/tmp/cvs-serv18795
Modified Files:
emboss.info emboss.patch
Log Message:
final fix for missing crypt.h
Index: emboss.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/emboss.patch,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- emboss.patch 30 Aug 2006 07:32:51 -0000 1.5
+++ emboss.patch 6 Apr 2007 21:17:42 -0000 1.6
@@ -1,2241 +1,24 @@
-diff -Naur EMBOSS-4.0.0/ajax/ajacd.c EMBOSS-4.0.0-patched/ajax/ajacd.c
---- EMBOSS-4.0.0/ajax/ajacd.c 2006-07-12 11:37:44.000000000 -0400
-+++ EMBOSS-4.0.0-patched/ajax/ajacd.c 2006-08-25 09:45:04.000000000 -0400
-@@ -2505,6 +2505,8 @@
- {"rdesshow", "N", "boolean", "Show description in the report"},
- {"rscoreshow", "Y", "boolean", "Show the score in the report"},
- {"rusashow", "N", "boolean", "Show the full USA in the report"},
-+ {"rmaxall", "0", "integer", "Maximum total hits to report"},
-+ {"rmaxseq", "0", "integer", "Maximum hits to report for one sequence"},
- {NULL, NULL, NULL, NULL}
- };
[...2224 lines suppressed...]
- ajPatternSeqGetMismatch(pat),&hits,&tidy);
-
- ajDebug ("embPatternSeqSearch: found %d hits\n",hits);
-- ajListReverse(list);
-+ if(!reverse)
-+ ajListReverse(list);
-+
- for(i=0;i<hits;++i)
- {
- ajListPop(list,(void **)&m);
- if (reverse)
-- sf = ajFeatNewIIRev(ftable, m->start, m->start + m->len - 1);
-+ sf = ajFeatNewIIRev(ftable, adj - m->start - m->len + 2,
-+ adj - m->start + 1);
- else
- sf = ajFeatNewII(ftable, m->start, m->start + m->len - 1);
++#if !defined(__APPLE__) && !defined(__FreeBSD__)
+ #include <crypt.h>
+ #endif
Index: emboss.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/emboss.info,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -d -r1.12 -r1.13
--- emboss.info 4 Apr 2007 15:17:51 -0000 1.12
+++ emboss.info 6 Apr 2007 21:17:42 -0000 1.13
@@ -1,6 +1,6 @@
Package: emboss
Version: 4.1.0
-Revision: 3
+Revision: 4
Depends: %N-ajax4-shlibs (>= %v-%r), %N-nucleus4-shlibs (>= %v-%r),
%N-plplot5-shlibs (>= %v-%r), x11, libpng3-shlibs, libjpeg-shlibs, gd2-shlibs,
system-java14
BuildDepends: libpng3, libjpeg, gd2, libiconv-dev, x11-dev, system-java14-dev
#Replaces: emboss (<< 2.7.1-2)
@@ -10,15 +10,12 @@
<<
Source-MD5: a08ed3834eb249162196df7ab889fd4c
SetCPPFLAGS: -Dstat64=stat
-#Patch: %n.patch
+Patch: %n.patch
PatchScript: <<
perl -pi -e 's,([<"])(pcre)(.*.h[>"]),\1EMBOSS/\2\3,' ajax/*
perl -pi -e 's,(pcre\S*\.h),EMBOSS/\1,g' ajax/Makefile.in
mkdir ajax/EMBOSS
mv ajax/pcre*.h ajax/EMBOSS
-# Replace crypt.h with blank
- perl -pi -e 's|\#include \<crypt.h\>||g' ajax/ajjava.c
- perl -pi -e 's|\#include \<crypt.h\>||g' emboss/jembossctl.c
<<
ConfigureParams:
--with-java=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home
--with-javaos=/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Home/include
--disable-dependency-tracking --libdir=%p/lib/EMBOSS
Installscript: <<
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